In my research I have noticed that the Nikon bodys I have been looking at (D40 & D60) have three points and the Canon bodys (1000D & 450D) have 7 & 9. Does this make a big difference or should it even be considered?

more AF points = More places to focus...
so the likes of a canon 1ds mkiii is 39 points i think... (i cba checking google sorry...)
Basically means there are 39 different places you can focus of without moving your camera / manual focusing.
Helps allot, Especially in circumstances your camera somehow wont tilt / position the object on the correct spot therefore you can chage the focus point to where-ever the object is in the viewfinder.

The value of more auto focus points is the ability to frame a shot, switch auto focus points to the one that is on the exact point in the shot you want the sharpest in focus, such as the eyes when shooting a portrait.

Fine for smallerer apertures. But I prefer to have the exact focus point of the photo dead on, not just close. Especially since I tend to shoot a lot of my natural light portraits at very large apertures.

So if you were choosing between the D50 and the 450D would the additional AF points steer you to the 450D?

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Not necessarily. There are many considerations that should go into a body choice besides focus points. They are just one part of the equation. The type of photography the body will be used for needs to be considered. Different photographic interest require different body features.

Fine for smallerer apertures. But I prefer to have the exact focus point of the photo dead on, not just close. Especially since I tend to shoot a lot of my natural light portraits at very large apertures.

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Easily compensated for by a wee movement of the focus ring. But this is my right hemisphere talking, which thinks more along the lines of "Um...yeah, whatever. Close enough."